Footage emerged Johnson lumping the state in with Iran when he raised concerns about “puppeteering” in the region.

He was addressing a conference in Rome when he talked of politicians “twisting and abusing religion” to further their political aims.

It is the second split between Johnson and May in under a week. On Sunday he said the prime minister was wrong to include student numbers in immigration figures.

Victoria Jones/PA Wire

The video, published by The Guardian, from the Med 2 event last week comes as Prime Minister Theresa May arrives back from a visit to the Gulf where she attended a dinner with the leaders of Saudi Arabia, Kuwait, the United Arab Emirates, Qatar, Bahrain and Oman.

Johnson said: “There are politicians who are twisting and abusing religion and different strains of the same religion in order to further their own political objectives. That’s one of the biggest political problems in the whole region.

“And the tragedy for me – and that’s why you have these proxy wars being fought the whole time in that area – is that there is not strong enough leadership in the countries themselves.”

The foreign secretary said there were not enough “big characters” in the region who were willing to “reach out beyond their Sunni or Shia” group.

He told the conference: “That’s why you’ve got the Saudis, Iran, everybody, moving in and puppeteering and playing proxy wars.”

A spokeswoman for the prime minister said May had “full confidence in the foreign secretary” but added Saudi Arabia was “a vital partner for the UK, particularly on counter-terrorism and, when you look at what is happening in the region, we are supportive of the Saudi-led coalition which is working in support of the legitimate government in Yemen against Houthi rebels”.

Asked if May shared the view of Johnson on the conflict, the prime minister’s spokeswoman said “they are not the government’s views on Saudi and its role in the region”.

A Foreign Office spokesman said: “As the foreign secretary made very clear on Sunday, we are allies with Saudi Arabia and support them in their efforts to secure their borders and protect their people. Any suggestion to the contrary is wrong and misinterpreting the facts.”